We have done the WGS for some strains and got a good coverage of data. We are trying to assembly the data. so for that we will be trying DNAstar, MIRA, and Newbler as Velvet not compatible and others are not open-sourced. So what do you think will give the best assembly and why? Have you done the WGS and if yes, which assembler did you use?
I would also include Spades in that list. We have seen some organism specific effects on the performance of assembler algorithms, so it is important to test a few, even if someone else found that on his or her IonTorrent data, algorithm A worked best. It could still be that for your data, algorithm B performs better.
For our whole genome data we have used newbler for ion torrent and we have got good result when compared with the whole genome data of 454 of the same species. Since both are long reads so Newbler will be suitable.
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